diff --git a/DESCRIPTION b/DESCRIPTION index 2cba6af..b9a36fb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: MungeSumstats Type: Package Title: Standardise summary statistics from GWAS -Version: 1.9.17 +Version: 1.9.18 Authors@R: c(person(given = "Alan", family = "Murphy", diff --git a/NEWS.md b/NEWS.md index 5b55a28..877421f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,35 @@ +## CHANGES IN VERSION 1.9.18 + +### New column header mappings +* "VARIANT_ID" and "RSIDS" --> "SNP" +* "P_BOLT_LMM" --> "P" +* "NCASES" --> "N_CAS" +* "N_EFFECTIVE", "N_INFORMATIVE", and "TOTAL_N" --> "N" +* "HET_P" --> "HETPVAL" +* "HET_ISQ" --> "HETISQT" +* "ALL_AF" --> "FRQ" +* "DIRECT" --> "DIRECTION" +* "ALT_EFFSIZE" --> "BETA" +* "INFORMATIVE_ALT_AC" --> "AC" + +### Fixed column header mappings +* Made all uncorrected header names uppercase and removed duplicates +* "TOTALSAMPLESIZE" now maps to "N" instead of "NSTUDY" +* "MAJORALLELE", "MAJOR_ALLELE", "MAJOR-ALLELE", and "MAJOR ALLELE" now map to +"A1" instead of "A2" +* Removed the mappings for "OR-A1", "OR.A1", "OR_A1", and "BETA1" because MSS +assumes that A2 is the effect allele +* Removed mappings for "A1FREQ", "A1FRQ", "AF1", "FREQ.A1.1000G.EUR", +"FREQ.A1.ESP.EUR", "FREQ.ALLELE1.HAPMAPCEU", "FREQ1", "FREQ1.HAPMAP", and +"FRQ_A1" because MSS defines "FRQ" to be the allele frequency of A2 +* Removed mappings for "CHR36", "BASE_GRCH36", "POSITION36", "POSGRCH36", +"BASEGRCH36", "POS36", "POS GRCH36", "POS.GRCH36", "POS-GRCH36", and "POS_GRCH36" +because MSS does not support the GRCh36 genome build +* Removed the ambiguous mapping "NMISS" -> "N" because "NMISS" can refer to the +number of samples with missing data +* Removed the ambiguous mapping "WEIGHT" -> "N" because "WEIGHT" can refer to +coefficient weights + ## CHANGES IN VERSION 1.9.17 ### Bug fix diff --git a/R/sysdata.rda b/R/sysdata.rda index 06028d0..785d0fd 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data/sumstatsColHeaders.rda b/data/sumstatsColHeaders.rda index 2960502..1458802 100644 Binary files a/data/sumstatsColHeaders.rda and b/data/sumstatsColHeaders.rda differ